Tick-borne encephalitis virus (TBEV) is an enveloped virus belonging to the family Flaviviridae, which causes severe disease of central nervous system in humans. The smooth virion surface is covered by envelope proteins (E-protein), that are together with the membrane proteins (M-protein) anchored in the virus lipid bilayer. During the viral life cycle, the immature non-infectious virus undergoes amaturation process. This process includes proteolytic cleavage of prM and a major reorganization of the envelope proteins on the viral surface.To determine the structure of immature TBEV particles, we purified them from infected tissue culture cells and used cryo-electron microscopy for visualization. The immature particles have “spiky” surface formed by the E-protein-prM-protein complex. We performed single-particle analysis and cryo-electron tomography to reveal the asymmetric nature of the TBEV immature particles. The symmetric, icosahedral, organization of the E-protein-prM-protein spikes on the particle surface is often disrupted by defects introduced during the assembly process of the immature particle. However, these irregularities do not hinder the subsequent maturation process and instead result in mature particles with empty patches in the “herring bone” organization of the mature viral surface.The results provide further insight into the viral maturation process which could be targeted in the future by specific antiviral drugs